I'm pretty new to computational biology, and I have been looking at Ken Dill's simplified "HP lattice" model of protein folding (which uses polar and hydrophobic monomers only, on a 2D or 3D grid).
The energy function he uses gives a value of -1 per hydrophobic monomer that is adjacent in space but not in sequence (described here: http://www3.interscience.wiley.com/cgi-bin/fulltext/36179/PDFSTART). I was wondering why the energy is not based on the amount of exposure of the hydrophobic residues to the surrounding solution instead (eg. the total number of empty points on the lattice adjacent to each "H").
Thanks for any pointers,
David F